# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0351 numbered 1 through 117 Created new target T0351 from T0351.a2m # command:CPU_time= 6.421 sec, elapsed time= 6.485 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g0uG/T0351-1g0uG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g0uG expands to /projects/compbio/data/pdb/1g0u.pdb.gz 1g0uG:# T0351 read from 1g0uG/T0351-1g0uG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g0uG read from 1g0uG/T0351-1g0uG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g0uG to template set # found chain 1g0uG in template set Warning: unaligning (T0351)P57 because last residue in template chain is (1g0uG)D240 T0351 5 :DAIMYK 1g0uG 192 :FAITHM # choosing archetypes in rotamer library T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1g0uG 216 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1g0uG 225 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g0uG/T0351-1g0uG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1g0uG/T0351-1g0uG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g0uG read from 1g0uG/T0351-1g0uG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g0uG in template set T0351 4 :YDAIMYK 1g0uG 191 :EFAITHM T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1g0uG 216 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1g0uG 225 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g0uG/T0351-1g0uG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1g0uG/T0351-1g0uG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g0uG read from 1g0uG/T0351-1g0uG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g0uG in template set T0351 3 :LYDA 1g0uG 197 :MIDA T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 30 :YIEKWNLRA 1g0uG 214 :VATKDKFFT T0351 41 :PTQAELETWWEELQK 1g0uG 224 :LSAENIEERLVAIAE Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/T0351-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.5 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0351 read from 2ap1A/T0351-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0351-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ap1A to template set # found chain 2ap1A in template set T0351 16 :SRKDFELRN 2ap1A 8 :GGTKIALGV T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWW 2ap1A 18 :DSTRRLQWEKRVPTPHTSYSAFLDAV T0351 79 :RKQLEELNKTLGN 2ap1A 44 :CELVEEADQRFGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/T0351-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 2ap1A/T0351-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0351-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set T0351 27 :NGSYIEKWNLRAPLPTQAELETW 2ap1A 20 :TRRLQWEKRVPTPHTSYSAFLDA T0351 78 :ARKQLEELNKTLG 2ap1A 43 :VCELVEEADQRFG Number of specific fragments extracted= 2 number of extra gaps= 0 total=17 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/T0351-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 2ap1A/T0351-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0351-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set T0351 17 :RKDFELR 2ap1A 9 :GTKIALG T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEEL 2ap1A 18 :DSTRRLQWEKRVPTPHTSYSAFLDAVCEL T0351 82 :LEELNKTLG 2ap1A 47 :VEEADQRFG Number of specific fragments extracted= 3 number of extra gaps= 0 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqaA/T0351-1xqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xqaA expands to /projects/compbio/data/pdb/1xqa.pdb.gz 1xqaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1xqaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1xqaA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1xqaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0351 read from 1xqaA/T0351-1xqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xqaA read from 1xqaA/T0351-1xqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xqaA to template set # found chain 1xqaA in template set T0351 15 :VSRKDFELRNDGNGSY 1xqaA 32 :RGNAFAVMRDNDGFIL T0351 31 :IEK 1xqaA 49 :LMK T0351 35 :NLRAP 1xqaA 54 :EVQYP T0351 40 :LPTQAELETWWEELQKN 1xqaA 67 :QESEEQVDKINQRLKED T0351 57 :PPYEP 1xqaA 85 :FLVEP Number of specific fragments extracted= 5 number of extra gaps= 0 total=25 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqaA/T0351-1xqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1xqaA/T0351-1xqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xqaA read from 1xqaA/T0351-1xqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xqaA in template set T0351 15 :VSRKDFELRNDGNGSY 1xqaA 32 :RGNAFAVMRDNDGFIL T0351 31 :IEK 1xqaA 49 :LMK T0351 36 :LRAP 1xqaA 55 :VQYP T0351 40 :LPTQAELETWWEELQKNPPYEPP 1xqaA 67 :QESEEQVDKINQRLKEDGFLVEP Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqaA/T0351-1xqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1xqaA/T0351-1xqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xqaA read from 1xqaA/T0351-1xqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xqaA in template set T0351 17 :RKDFELRNDGNGSYIEKWNLRAPLPTQAELETWWEELQKNP 1xqaA 44 :GFILTLMKGKEVQYPKTFHVGFPQESEEQVDKINQRLKEDG T0351 58 :PYEPP 1xqaA 86 :LVEPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypA/T0351-1rypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rypA expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1rypA:# T0351 read from 1rypA/T0351-1rypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rypA read from 1rypA/T0351-1rypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rypA to template set # found chain 1rypA in template set Warning: unaligning (T0351)P57 because last residue in template chain is (1rypA)D252 T0351 5 :DAIMYK 1rypA 205 :FAITHM T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1rypA 229 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1rypA 237 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=35 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypA/T0351-1rypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1rypA/T0351-1rypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rypA read from 1rypA/T0351-1rypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rypA in template set T0351 4 :YDAIMYK 1rypA 204 :EFAITHM T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1rypA 229 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1rypA 237 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypA/T0351-1rypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1rypA/T0351-1rypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rypA read from 1rypA/T0351-1rypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rypA in template set T0351 3 :LYDA 1rypA 210 :MIDA T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 30 :YIEKWNLRA 1rypA 227 :VATKDKFFT T0351 41 :PTQAELETWWEELQK 1rypA 236 :LSAENIEERLVAIAE Number of specific fragments extracted= 4 number of extra gaps= 0 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gl6A/T0351-1gl6A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gl6A expands to /projects/compbio/data/pdb/1gl6.pdb.gz 1gl6A:# T0351 read from 1gl6A/T0351-1gl6A-t06-local-adpstyle5.a2m # 1gl6A read from 1gl6A/T0351-1gl6A-t06-local-adpstyle5.a2m # adding 1gl6A to template set # found chain 1gl6A in template set T0351 11 :YPNAVSRKDFELRNDGNGSYIEKWNLR 1gl6A 294 :MPDGDFSIRSWLEDPNGGNLFITWRED T0351 40 :LPTQAELETWWEELQKNPPYEPPDQVELLAQELSQEKLARKQLEELNKT 1gl6A 322 :GPALRPLISAWVDVVCTSILSLPEEPKRRLWLFIDELASLEKLASLADA Number of specific fragments extracted= 2 number of extra gaps= 0 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exrA/T0351-1exrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1exrA/T0351-1exrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exrA read from 1exrA/T0351-1exrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1exrA in training set T0351 24 :NDGNGSY 1exrA 21 :KDGDGTI T0351 38 :APLPTQAELETWWEELQKNPPYE 1exrA 40 :GQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELS 1exrA 66 :PEFLSLMARKMK T0351 74 :QEKLARKQLEELNKTLGNEL 1exrA 81 :SEEELIEAFKVFDRDGNGLI T0351 94 :SDIKLSLLSLKGDYAELE 1exrA 103 :AELRHVMTNLGEKLTDDE Number of specific fragments extracted= 5 number of extra gaps= 0 total=50 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exrA/T0351-1exrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1exrA/T0351-1exrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exrA read from 1exrA/T0351-1exrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1exrA in training set T0351 38 :APLPTQAELETWWEELQKNPPYE 1exrA 40 :GQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELSQEKLARK 1exrA 66 :PEFLSLMARKMKEQDSEEE T0351 82 :LEELNKTL 1exrA 85 :LIEAFKVF T0351 90 :GNELSDI 1exrA 102 :AAELRHV T0351 98 :LSLLSLKGDYAELEH 1exrA 109 :MTNLGEKLTDDEVDE Number of specific fragments extracted= 5 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exrA/T0351-1exrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1exrA/T0351-1exrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exrA read from 1exrA/T0351-1exrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1exrA in training set T0351 24 :NDGNGSY 1exrA 21 :KDGDGTI T0351 39 :PLPTQAELETWWEELQKNPPYE 1exrA 41 :QNPTEAELQDMINEVDADGNGT T0351 61 :PPDQVELLAQELSQEKLARKQLEELNK 1exrA 65 :FPEFLSLMARKMKEQDSEEELIEAFKV T0351 89 :L 1exrA 92 :F T0351 90 :GNELSDI 1exrA 102 :AAELRHV Number of specific fragments extracted= 5 number of extra gaps= 0 total=60 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahqA/T0351-2ahqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ahqA expands to /projects/compbio/data/pdb/2ahq.pdb.gz 2ahqA:# T0351 read from 2ahqA/T0351-2ahqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahqA read from 2ahqA/T0351-2ahqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ahqA to template set # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 36 :LRAPLPTQAELETWWEELQKNPPYEPPDQVELLAQELS 2ahqA 11 :ESAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILK T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 2 number of extra gaps= 0 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahqA/T0351-2ahqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 2ahqA/T0351-2ahqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahqA read from 2ahqA/T0351-2ahqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 37 :RAPLPTQAELETWWEELQKN 2ahqA 12 :SAEGLTQGELMKLIKEIVEN T0351 57 :PPYEPP 2ahqA 33 :DKRKPY T0351 64 :QVELLAQELSQ 2ahqA 39 :SDQEIANILKE T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahqA/T0351-2ahqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 2ahqA/T0351-2ahqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahqA read from 2ahqA/T0351-2ahqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 37 :RAPLPTQAELETWWEELQKNPPYEPPDQVELLAQELSQ 2ahqA 12 :SAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKE T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f1sA/T0351-1f1sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f1sA expands to /projects/compbio/data/pdb/1f1s.pdb.gz 1f1sA:# T0351 read from 1f1sA/T0351-1f1sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f1sA read from 1f1sA/T0351-1f1sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f1sA to template set # found chain 1f1sA in template set T0351 13 :NAVSRKDFELR 1f1sA 220 :NATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQK 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWND T0351 57 :PPYEP 1f1sA 269 :YDTND T0351 63 :DQVELLAQEL 1f1sA 274 :SNMQKLNQKL T0351 75 :EKLARKQLEE 1f1sA 284 :DETNAKNIEA Number of specific fragments extracted= 5 number of extra gaps= 0 total=73 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f1sA/T0351-1f1sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1f1sA/T0351-1f1sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f1sA read from 1f1sA/T0351-1f1sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f1sA in template set T0351 11 :YPNAVSRKDFELR 1f1sA 218 :YPNATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQKN 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWNDV T0351 57 :PPYEPPDQVELL 1f1sA 269 :YDTNDSNMQKLN T0351 70 :Q 1f1sA 281 :Q T0351 77 :LARKQLEELNKTL 1f1sA 282 :KLDETNAKNIEAI Number of specific fragments extracted= 5 number of extra gaps= 0 total=78 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f1sA/T0351-1f1sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1f1sA/T0351-1f1sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f1sA read from 1f1sA/T0351-1f1sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f1sA in template set T0351 12 :PNAVSRKDFELR 1f1sA 219 :PNATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQK 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWND T0351 57 :PPYE 1f1sA 269 :YDTN T0351 62 :PDQVELL 1f1sA 273 :DSNMQKL T0351 82 :LEELNKTLGNELSDIKL 1f1sA 280 :NQKLDETNAKNIEAIKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=83 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0351-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0351 read from 1swvA/T0351-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0351-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1swvA to template set # found chain 1swvA in template set T0351 38 :APLPTQAELETWWEELQKN 1swvA 75 :RQLPTEADIQEMYEEFEEI T0351 57 :PPYEPP 1swvA 99 :PRYASP T0351 72 :LSQEKLARKQLEELN 1swvA 105 :INGVKEVIASLRERG T0351 90 :GNELSDIKLSLLSLKG 1swvA 129 :TREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=87 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0351-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1swvA/T0351-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0351-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set T0351 38 :APLPTQAELETWWEELQK 1swvA 75 :RQLPTEADIQEMYEEFEE T0351 63 :DQVELLAQE 1swvA 93 :ILFAILPRY T0351 72 :LSQEKLARKQLEEL 1swvA 105 :INGVKEVIASLRER T0351 89 :LGNELSDIKLSLLSLKG 1swvA 128 :YTREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=91 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/T0351-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1swvA/T0351-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0351-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set T0351 39 :PLPTQAELETWWEELQK 1swvA 76 :QLPTEADIQEMYEEFEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=92 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0351-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0351 read from 1rqlA/T0351-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0351-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rqlA to template set # found chain 1rqlA in template set T0351 38 :APLPTQAELETWWEELQKN 1rqlA 75 :RQLPTEADIQEMYEEFEEI T0351 57 :PPYEPP 1rqlA 99 :PRYASP T0351 72 :LSQEKLARKQLEELN 1rqlA 105 :INAVKEVIASLRERG T0351 90 :GNELSDIKLSLLSLKG 1rqlA 129 :TREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0351-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1rqlA/T0351-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0351-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set T0351 38 :APLPTQAELETWWEELQKN 1rqlA 75 :RQLPTEADIQEMYEEFEEI T0351 64 :QVELLAQELS 1rqlA 94 :LFAILPRYAS T0351 74 :QEKLARKQLEEL 1rqlA 107 :AVKEVIASLRER T0351 89 :LGNELSDIKLSLLSLKG 1rqlA 128 :YTREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/T0351-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1rqlA/T0351-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0351-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set T0351 39 :PLPTQAELETWWEELQK 1rqlA 76 :QLPTEADIQEMYEEFEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=101 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yirA/T0351-1yirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yirA expands to /projects/compbio/data/pdb/1yir.pdb.gz 1yirA:# T0351 read from 1yirA/T0351-1yirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yirA read from 1yirA/T0351-1yirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yirA to template set # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNA 1yirA 26 :MMQAVLHNYPNA T0351 17 :RKDFELRNDGNGSY 1yirA 38 :EVEWEFRCRNQEDL T0351 43 :QAELETWWEELQKNP 1yirA 55 :LPAIREQLEYLAGLA T0351 60 :EPPDQVELLAQ 1yirA 70 :ISDEQLAFLER T0351 75 :EKLARKQL 1yirA 85 :APDFIRFL Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yirA/T0351-1yirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1yirA/T0351-1yirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yirA read from 1yirA/T0351-1yirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNAVSRKDFELRNDGNG 1yirA 26 :MMQAVLHNYPNAEVEWEFRCRNQEDL T0351 43 :QAELETWWEELQKNP 1yirA 55 :LPAIREQLEYLAGLA T0351 60 :EPPDQVELLAQ 1yirA 70 :ISDEQLAFLER T0351 76 :KLARKQLE 1yirA 86 :PDFIRFLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=110 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yirA/T0351-1yirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1yirA/T0351-1yirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yirA read from 1yirA/T0351-1yirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNAV 1yirA 26 :MMQAVLHNYPNAE T0351 22 :L 1yirA 39 :V T0351 33 :KWNLRAPLPT 1yirA 40 :EWEFRCRNQE T0351 44 :AELETWWEELQKNPP 1yirA 56 :PAIREQLEYLAGLAI T0351 61 :PPDQVELLAQ 1yirA 71 :SDEQLAFLER T0351 88 :TLGNELSDIKLS 1yirA 87 :DFIRFLGLFRFN Number of specific fragments extracted= 6 number of extra gaps= 0 total=116 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrvA/T0351-1yrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yrvA expands to /projects/compbio/data/pdb/1yrv.pdb.gz 1yrvA:# T0351 read from 1yrvA/T0351-1yrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrvA read from 1yrvA/T0351-1yrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yrvA to template set # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 32 :EKWNLRAP 1yrvA 97 :EKWNTNYT T0351 46 :LETWWEELQK 1yrvA 105 :LSSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrvA/T0351-1yrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1yrvA/T0351-1yrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrvA read from 1yrvA/T0351-1yrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 46 :LETWWEELQK 1yrvA 105 :LSSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=121 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrvA/T0351-1yrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0351 read from 1yrvA/T0351-1yrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrvA read from 1yrvA/T0351-1yrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 47 :ETWWEELQK 1yrvA 106 :SSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=123 Will force an alignment to be made, even if fragment is small Number of alignments=34 # command:CPU_time= 13.450 sec, elapsed time= 14.197 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 34 Adding 6786 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.468 sec, elapsed time= 14.216 sec. # command:Reading probabilities from T0351.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 6.317 Optimizing... Probability sum: -208.590, CN propb: -208.590 weights: 0.221 constraints: 147 # command:CPU_time= 13.835 sec, elapsed time= 14.608 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 147 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 147 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 226 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 226 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 5513 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 5513 # command:CPU_time= 13.942 sec, elapsed time= 14.805 sec. # command: